Is the trans up shifted by electrical servos or by hydraulic like the old 727? If elec then why not just use micro switches to up shift and down shift( full manual ). The speed sensor iis inside trans and works with the abs sensors plus main controller. Reason I know the mechanic next door spent two months with the help from the Dodge shop trying to find the problem with a 2011 Charger. The trans would go into limp mode, tried everything, two trans, new sensors, changed tires. Come to find out the previous owner had changed to an SRT8 rear(3.06 ratio) and main controller was programmed for a 2.65, so the sensors couldn't jive and kicked it into limp, even the main engineers from Chrysler couldn't figure this out. Changed back to an original rear and trans worked fine.But chrysler did say the tires had to be within 5% of stock size to work properly(same as changing gear ratio). We think the rear package came with a chip box but was lost with selling the car to dealer to used dealer. As far as using Jeep trans I think they are independent (bolted solid to frame) so no u-joint either, I didn't see the type of slip u-joint you used in your build up pics other than the aluminum piece.
Edit; got the original trans and going to pull it down to see if my idea would work.